References
- Borsani O, Valpuesta V, Botella MA. Developing salt tolerant plants in a new century: a molecular biology approach. Plant Cell, Tissue Organ Culture. 2003;73(2):101–115.
- Mallik S, Nayak M, Sahu BB, et al. Response of antioxidant enzymes to high NaCl concentration in different salt-tolerant plants. Biologia Plant. 2011;55(1):191–195.
- Al Hassan M, Estrelles E, Soriano P, et al. Unraveling salt tolerance mechanisms in halophytes: A comparative study on four Mediterranean Limonium species with different geographic distribution patterns. Front Plant Sci. 2017;8:1438.
- Gharbi E, Martinez JP, Benahmed H, et al. Phytohormone profiling in relation to osmotic adjustment in NaCl-treated plants of the halophyte tomato wild relative species Solanum chilense comparatively to the cultivated glycophyte Solanum lycopersicum. Plant Sci. 2017;258:77–89.
- Nikalje GC, Variyar PS, Joshi MV, et al. "Temporal and spatial changes in ion homeostasis and accumulation of flavanoids and glycolipid in a halophyte Sesuvium portulacastrum (L.) L. PLoS One. 2018;13(4):e0193394.
- Rahman MM, Rahman MA, Miah MG, et al. Mechanistic insight into salt tolerance of Acacia auriculiformis: the importance of ion selectivity, osmoprotection, tissue tolerance, and Na + exclusion. Front Plant Sci. 2017;8:155.
- Burman U, Garg BK, and, Kathju S. Interactive effects of thiourea and phosphorus on clusterbean under water stress. Biologia Plant. 2004;48(1):61–65.
- Ashraf MY, Akhtar K, Sarwar G, et al. Role of the rooting system in salt tolerance potential of different guar accessions. Agron Sustain Dev. 2005;25(2):243–249.
- Francois LE, Donovan TJ, Maas EV. Salinity effects on emergence, vegetative growth, and seed yield of guar. Agronj. 1990;82(3):587–592.
- Wang Z, Gerstein M, and, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.
- An YM, Song LL, Liu YR, et al. De Novo transcriptional analysis of Alfalfa in response to saline-alkaline stress. Front Plant Sci. 2016;7:931.
- Diray-Arce J, Clement M, Gul B, et al. Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics. 2015;16(1):353.
- Hess M, Wildhagen H, Junker LV, et al. Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat. BMC Genomics. 2016;17(1):682.
- Sharma R, Mishra M, Gupta B, et al. De Novo assembly and characterization of stress transcriptome in a salinity-tolerant variety CS52 of Brassica juncea. PLoS One. 2015;10(5):e0126783.
- Woldesemayat AA, and, Ntwasa M. Pathways and network based analysis of candidate genes to reveal cross-talk and specificity in the Sorghum (Sorghum bicolor (L.) Moench) responses to drought and it’s co-occurring stresses. Front Genet. 2018;9:557.
- Angela Pérez-Novo C, Claeys C, Speleman F, et al. Impact of RNA quality on reference gene expression stability. Biotechniques. 2005;39(1):52–56.
- Gehrig HH, Winter K, Cushman J, et al. An improved RNA isolation method for succulent plant species rich in polyphenols and polysaccharides. Plant Mol Biol Rep. 2000;18(4):369–376.
- Katterman FRH, Shattuck VI. An effective method of DNA isolation from the mature leaves of Gossypium species that contain large amounts of phenolic terpenoids and tannins. Prep Biochem. 1983;13(4):347–359.
- Levi A, Galau GA, Wetzstein HY. A rapid procedure for the isolation of RNA from high-phenolic-containing tissues of pecan. HortSci. 1992;27(12):1316–1318.
- Sambrook HC, Fritsch, EF, Maniatis, T. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
- Agrawal AA. Current trends in the evolutionary ecology of plant defence. Functional Ecol. 2011;25(2):420–432.
- Berenbaum MR, Zangerl AR. Facing the future of plant-insect interaction research: le retour à la “raison d’être". Plant Physiol. 2008;146(3):804–811.
- Loomis WD. 1974. Overcoming problems of phenolics and quinones in the isolation of plant enzymes and organelles. Methods in enzymology, 31, 528–544. https://doi.org/10.1016/0076-6879(74)31057-9.
- Macel M, Van Dam NM, Keurentjes JJ. Metabolomics: the chemistry between ecology and genetics. Mol Ecol Resour. 2010;10(4):583–593.
- Sharma AD, Gill PK, Singh P. RNA isolation from plant tissues rich in polysaccharides. Anal Biochem. 2003;314(2):319–321.
- Walter J, Hein R, Auge H, et al. How do extreme drought and plant community composition affect host plant metabolites and herbivore performance?Arthropod-Plant Inter. 2012;6(1):15–25.
- Bilgin DD, DeLucia EH, Clough SJ. A robust plant RNA isolation method suitable for Affymetrix GeneChip analysis and quantitative real-time RT-PCR. Nat Protoc. 2009;4(3):333–340.
- Gayral P, Weinert L, Chiari Y, et al. Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals. Mol Ecol Resour. 2011;11(4):650–661.
- Johnson MT, Carpenter EJ, Tian Z, et al. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One. 2012;7(11):e50226.
- Behnam B, Bohorquez-Chaux A, Castaneda OF, et al. An optimized isolation protocol yields high-quality RNA from cassava tissues (Manihot esculenta Crantz). FEBS Open Bio. 2019;9(4):814–825.
- Liu L, Han R, Yu N, et al. A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense. PloS One. 2018;13(5):e0196592.
- Sellin MJ, Kiss AJ, Smith AW, et al. A comparison of commercially-available automated and manual extraction kits for the isolation of total RNA from small tissue samples. BMC Biotechnol. 2014;14(1):94–94.
- Iandolino AB, Goes Da Silva F, Lim H, et al. High-quality RNA, cDNA, and derived EST libraries from grapevine (Vitis vinifera L.). Plant Mol Biol Rep. 2004;22(3):269–278.
- Matsubara T, Soh J, Morita M, et al. DV200 Index for Assessing RNA integrity in next-generation sequencing. Biomed Res Int. 2020;2020:9349132.
- Alshameri A, Al-Qurainy F, Khan S, et al. Appraisal of guar [Cyamopsis tetragonoloba (l.) Taub.] accessions for forage purpose under the typical Saudi Arabian environmental conditions encompassing high temperature, salinity and drought. Pak J Bot. 2017;49(4):1405–1413.
- Kanani P, Shukla YM, Modi AR, et al. Standardization of an efficient protocol for isolation of RNA from Cuminum cyminum. J King Saud Univ-Sci. 2019;31(4):1202–1207.
- Imbeaud S, Graudens E, Boulanger V, et al. Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res. 2005;33(6):e56–e56.
- Padmanaban A, Ruediger S, Charmian C. RNA quality control using the agilent 2200 TapeStation system–assessment of the RIN e quality metric (Application note No.5991-0023EN). Agilent Technologies Application Notes. 2012. Retrieved from https://hpst.cz/sites/default/files/oldfiles/rna-quality-control-using-agilent-2200-tapestation-system-assessmentrine-quality-metric.pdf
- Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Cambridge, United Kingdom: Babraham Bioinformatics, Babraham Institute.
- Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–652.
- Haas BJ, Papanicolaou A, Yassour M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–1512.
- Patil CG. Nuclear DNA amount variation in Cyamopsis DC (Fabaceae). Cytologia. 2004;69(1):59–62.
- Minhas PS, Rane J, and RK. Pasala 2017. Abiotic stress management for resilient agriculture. New York, USA: Springer.
- Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell. 2015;58(4):586–597.
- Kukurba KR, Montgomery SB. RNA sequencing and analysis. Cold Spring Harb Protoc. 2015;2015(11):pdb.top084970. pdb. top084970.
- Almarza J, Morales S, Rincon L, et al. Urea as the only inactivator of RNase for extraction of total RNA from plant and animal tissues. Anal Biochem. 2006;358(1):143–145.
- Bekesiova I, Nap J-P, and, Mlynarova L. Isolation of high quality DNA and RNA from leaves of the carnivorous plant Drosera rotundifolia. Plant Mol Biol Rep. 1999;17(3):269–277.
- Chang S, Puryear J, Cairney J. A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep. 1993;11(2):113–116.
- Kiefer E, Heller W, Ernst D. A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites. Plant Mol Biol Rep. 2000;18(1):33–39.
- Geuna F, Hartings H, Scienza A. A new method for rapid extraction of high quality RNA from recalcitrant tissues of grapevine. Plant Mol Biol Rep. 1998;16(1):61–67.
- Chomczynski P, Sacchi N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on . Nat Protoc. 2006;1(2):581–585.
- Chomzynski P. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162(1):156–159.
- Puissant C, Houdebine LM. An improvement of the single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Biotechniques. 1990;8(2):148–149.
- Newbury HJ, Possingham JV. Factors affecting the extraction of intact ribonucleic Acid from plant tissues containing interfering phenolic compounds. Plant Physiol. 1977;60(4):543–547.
- Wan C-Y, Wilkins TA. A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L.). Anal Biochem. 1994;223(1):7–12.
- Jakovljević KV, Spasić MR, Mališić EJ, et al. Comparison of phenol-based and alternative RNA isolation methods for gene expression analyses. J Serb Chem Soc. 2010;75(8):1053–1061.
- Russell DW, Sambrook J. 2001. Molecular cloning: a laboratory manual. Vol. 1. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
- Tavares L, Alves PM, Ferreira RB, et al. Comparison of different methods for DNA-free RNA isolation from SK-N-MC neuroblastoma. BMC Res Notes. 2011;4(1):3.doi:10.1186/1756-0500-4-3.
- Zhen L-N, Kang W, Ying-Jun Z, et al. A method for high-quality RNA extraction from tall fescue. Afr J Biotechnol. 2011;10(37):7161–7165.
- De Coaña YP, Parody N, Fernández-Caldas E, et al. A Modified Protocol for RNA isolation from high polysaccharide containing Cupressus arizonica Pollen. Applications for RT-PCR and phage display library construction. Mol Biotechnol. 2010;44(2):127–132.
- Wilfinger WW, Mackey K, and, Chomczynski P. Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechniques. 1997;22(3):4746. 478-81.
- Pester D, Milcevicova R, Schaffer J, et al. Erwinia amylovora expresses fast and simultaneously hrp/dsp virulence genes during flower infection on apple trees. PLoS One. 2012;7(3):e32583.
- Schroeder A, Mueller O, Stocker S, et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol. 2006;7(1):3.
- Vasanthaiah HK, Katam R, Sheikh MB. Efficient protocol for isolation of functional RNA from different grape tissue rich in polyphenols and polysaccharides for gene expression studies. Electron J Biotechnol. 2008;11(3):0–51.
- Babu S, Gassmann M. 2011. Assessing integrity of plant RNA with the Agilent 2100 Bioanalyzer. California, USA: Agilent Technologies.
- Pereira MA, Imada EL, Guedes RLM. RNA-seq: applications and best practices. In Applications of RNA-Seq omics strategies-from microorganisms to human health. 2017. p. 3–36. London, United Kingdom: IntechOpen.
- Hall TC. 2018. Nucleic acids in plants: Volume I. Florida, USA: CRC Press.
- Smart M, Roden LC. A small-scale RNA isolation protocol useful for high-throughput extractions from recalcitrant plants. S Afr J Bot. 2010;76(2):375–379.
- Kim WS, Haj-Ahmad Y. Evaluation of Plant RNA Integrity Number (RIN) generated using an Agilent BioAnalyzer 2100. Application Note 80 Plant/Fungi RNA Sample Preparation - Norgen Biotek Corp. 2016. Retrieved from https://norgenbiotek.com/sites/default/files/resources/App-Note-80-Plant-RNA-RIN.pdf